From what I understand, HTML 5 is not due to be approved/released officially for another decade or so, and is not supported by all browsers. HTML5 may not be an option, but depending on what your Flash does, you may be able to pull off something similar using all the different jQuery/CSS/HTML/etc stuff that's needed to try to emulate Flash.

You may just want to wait to see if Apple changes their mind about being so antagonistic wrt any technology they don't own.